rs1942043

chr2-134797922-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000392929.6(CCNT2-AS1):n.427-62341A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,278 control chromosomes in the GnomAD database, including 292 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.049 (292 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCNT2-AS1 ENST00000392929.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

CCNT2-AS1 (HGNC:40130): (CCNT2 antisense RNA 1)

VDAC2P4 (HGNC:51932): (VDAC2 pseudogene 4)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNT2-AS1	ENST00000392929.6	n.427-62341A>G		intron_variant, non_coding_transcript_variant		4
VDAC2P4	ENST00000452925.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7449 AN: 152160 Hom.: 288 Cov.: 32

Gnomad AFR AF: 0.0655

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0615

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0516

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0491 AC: 7478 AN: 152278 Hom.: 292 Cov.: 32 AF XY: 0.0508 AC XY: 3780 AN XY: 74478

Gnomad4 AFR AF: 0.0658

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0615

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.0374

Gnomad4 NFE AF: 0.0207

Gnomad4 OTH AF: 0.0525

Alfa AF: 0.0310 Hom.: 35

Bravo AF: 0.0569

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.9
Dann	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1942043; hg19: chr2-135555492;